Measurement of the heart rate variability enables to assess the activity of the autonomous nervous system. The aim of the study was to evaluate the possible relationship between clinical status, serum sodium (Na), potassium (K), calcium (Ca), magnesium concentrations and HRV in children with mitral valve prolapse. The study group consisted of 151 children with MVP (age +/- SD: 12.2 +/- 3.1 years). Thirty patients out of the MVP group were symptomatic and 121 were asymptomatic. The total number of 165 healthy children (age +/- SD: 12.3 +/- 3.7 years) were included into the control group. We assessed power spectrum of HRV (low frequency component--LF, high frequency component--HF, and LF/HF ratio) from 5-minute recording during daytime and night. Serum Mg (p < 0.00001) and K (p < 0.03) concentrations were significantly lower in MVP group as compared to healthy children. A marked decrease in Mg concentration was observed in symptomatic children with MVP as compared to asymptomatic patients (p < 0.0001). A significant positive correlation was found between Mg concentration and HF and HF n.u. components (daytime and night) and significant negative correlation was observed between Mg concentration and LF and LF n.u. (daytime and night) parameters and LF/HF ratio (daytime and night). Symptomatic children with MVP had significantly higher LF n.u. and LF/HF ratio and a lower HF n.u. as compared to asymptomatic patients. The autonomic changes in MVP children (reduction in parasympathetic tone with sympathetic predominance) were associated with decreased serum Mg concentration and higher prevalence of clinical symptoms. Mg supplementation seems to be a prudent approach in symptomatic children with MVP.